A systems biology approach to studying the role of microbes in human health
Open accessAbstract
Host-microbe interactions play a crucial role in human health and disease. Of the various systems biology approaches, reconstruction of genome-scale metabolic networks combined with constraint-based modeling has been particularly successful at in silico predicting the phenotypic characteristics of single organisms. Here, we summarize recent studies, which have applied this approach to investigate microbe-microbe and host-microbe metabolic interactions. This approach can be also expanded to investigate the properties of an entire microbial community, as well as single organisms within the community. We illustrate that the constraint-based modeling approach is suitable to model host-microbe interactions at molecular resolution and will enable systematic investigation of metabolic links between the human host and its microbes. Such host-microbe models, combined with experimental data, will ultimately further our understanding of how microbes influence human health.
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Flux Balance Analysis models have been used to predict and understand the behavior of microbes given their environment.
“For instance, Flux Balance Analysis (FBA) models have been used to predict and understand the behavior of microbes given their environment (Orth et al., 2010;Thiele et al., 2013;Zelezniak et al., 2015).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Thiele et al., 2013
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What is flux balance analysis?
Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903 · see citing works
Self-citationQuantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835 · see citing works
Self-citationA protocol for generating a high-quality genome-scale metabolic reconstruction
Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789 · see citing works
Self-citationHigh-throughput generation, optimization and analysis of genome-scale metabolic models
Henry, C. S., DeJongh, M., Best, A. A., Frybarger, P. M., Linsay, B., & Stevens, R. L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1672 · Cited by 1,090 · see citing works
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
Feist, A. M., & Palsson, B. Ø. (2008) · Nature Biotechnology · doi:10.1038/nbt1401 · Cited by 545 · cited 1× · see citing works
“com many reaction rates, kinetic parameters, metabolite and enzyme concentrations, the COBRA approach permits the computation of phenotypic and physiological properties of the reconstructed networks [18,19].”
Barrila, J., Radtke, A. L., Crabbé, A., Sarker, S. F., Herbst-Kralovetz, M. M., Ott, C. M., & Nickerson, C. A. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2423 · Cited by 302 · see citing works
Thiele, I., Jamshidi, N., Fleming, R. M. T., & Palsson, B. Ø. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000312 · Cited by 182 · see citing works
Self-citationA detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Sigurdsson, M. I., Jamshidi, N., Steingrimsson, E., Thiele, I., & Palsson, B. Ø. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-140 · Cited by 154 · see citing works
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Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286 · see citing works
Modeling metabolism of the human gut microbiome
Magnúsdóttir, S., & Thiele, I. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.12.005 · Cited by 127 · see citing works
Self-citationAnoxic Conditions Promote Species-Specific Mutualism between Gut Microbes <i>In Silico</i>
Heinken, A., & Thiele, I. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.00101-15 · Cited by 123 · see citing works
Metabolic network modeling of microbial communities
Biggs, M. B., Medlock, G. L., Kolling, G. L., & Papin, J. A. (2015) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1308 · Cited by 124 · see citing works
The primary biological network of Bifidobacterium in the gut
Luo, J., Li, Y., Xie, J., Gao, L., Liu, L., Ou, S., Chen, L., & Peng, X. (2018) · FEMS Microbiology Letters · doi:10.1093/femsle/fny057 · Cited by 36 · see citing works
- Authors
- Thiele, I., Heinken, A., & Fleming, R. M.
- Affiliations
- University of Iceland (IS)
- Corresponding author
- Thiele, Ines
- Venue
- Current Opinion in Biotechnology
- Publisher
- Elsevier BV
- Published
- 2013-02
- Volume
- 24
- Issue
- 1
- Pages
- 4-12
- ISSN
- 0958-1669 (ISSN-L)
- OpenAlex
- W2063361228
- Cited by
- 114
- References
- 8
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 11 · 2023: 7 · 2022: 5 · 2021: 7 · 2020: 6 · 2019: 11 · 2018: 9 · 2017: 12 · 2016: 8 · 2015: 13 · 2014: 9 · 2013: 4 · 2012: 1
- FWCI
- 0.79
- Type
- journal article
- Language
- en
- Open access
- green
- orbilu.uni.lu
- Licence
- Locations
- Current Opinion in Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Open Repository and Bibliography (University of Luxembourg) (submittedVersion, cc-by-nc-sa)
- Hirsla (Landspítali University Hospital) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- host-microbe interactions, microbial communities, constraint-based modeling, genome-scale metabolic networks, human health, microbial metabolism
- MeSH terms
- Computer Simulation, Health, Humans, Intestines, Models, Biological, Biofilms, Systems Biology, Metabolic Networks and Pathways, Host-Pathogen Interactions, Microbial Interactions
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